I agree with what everyone's been saying in here that the heightened security is because of the leak/early release of the game. When a company is trying to make money, anything that could possibly compromise the profit resulting from their product is usually attacked mercilessly. This is probably because once you have a medium that you have put your work into (say a DVD for example), once that medium has switched over to a more accessible medium (i.e. the internet via pirated files) it becomes near impossible to police and profits relating to the original will obviously fall soon after.. which brings me to my point:
Pepakura files are already on the internet via a file (and program) that's readily available and accessible to everyone. This means they area already very wide spread, or capable of being wide spread and as such, are pretty much impossible for microsoft to completely police. IMHO, I don't think this (to what I perceive will be a small) stint of heightened security will really affect pep files, the creation of them, or the distribution of them.
As evidenced just in this thread alone, many people store pep files on their computer for future use, building an index, etc. Microsoft would never be able to stop that

. I myself have saved all the necessary files to build up the ODST, Mk. V and Mk. VI suits HD, MD and LD where applicable.. if push came to shove, I'd happily be willing to provide distribution of all these files to those who would use them for their proper purposes, with the creator's permission willing of course.
In short, I say PEP FILES FOR ALL!!!!! If pep files were really ever banned, the creation of pep files could even take on a cool underground movement type thing haha.